Members of highly social species decode, interpret, and react to the emotion of a conspecific depending on whether the other belongs to the same (ingroup) or different (outgroup) social group. While studies indicate that consciously perceived emotional stimuli drive social categorization, information about how implicit emotional stimuli and specific physiological signatures affect social categorization is lacking. We addressed this issue by exploring whether subliminal and supraliminal affective priming can influence the categorization of neutral faces as ingroup versus outgroup. Functional infrared thermal imaging was used to investigate whether the effect of affective priming on the categorization decision was moderated by the activation of the sympathetic nervous system (SNS). During the subliminal condition, we found that stronger SNS activation after positive or negative affective primes induced ingroup and outgroup face categorization, respectively. The exact opposite pattern (i.e. outgroup after positive and ingroup after negative primes) was observed in the supraliminal condition. We also found that misattribution effects were stronger in people with low emotional awareness, suggesting that this trait moderates how one recognizes SNS signals and employs them for unrelated decisions. Our results allow the remarkable implication that low-level affective reactions coupled with sympathetic activation may bias social categorization.